9CGY | pdb_00009cgy

Structure of the Pel modification enzyme PelA from Pseudomonas thermotolerans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation   3D Report Full Report


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Literature

Structural and functional analysis of Pseudomonas aeruginosa PelA provides insight into the modification of the Pel exopolysaccharide.

Van Loon, J.C.Le Mauff, F.Vargas, M.A.Gilbert, S.Pfoh, R.Morrison, Z.A.Razvi, E.Nitz, M.Sheppard, D.C.Howell, P.L.

(2025) J Biological Chem 301: 108432-108432

  • DOI: https://doi.org/10.1016/j.jbc.2025.108432
  • Primary Citation of Related Structures:  
    9CGY

  • PubMed Abstract: 

    A major biofilm matrix determinant of Pseudomonas aeruginosa is the partially deacetylated α-1,4 linked N-acetylgalactosamine polymer, Pel. After synthesis and transport of the GalNAc polysaccharide across the inner membrane, PelA partially deacetylates and hydrolyzes Pel before its export out of the cell via PelB. While the Pel modification and export proteins are known to interact in the periplasm, it is unclear how the interaction of PelA and PelB coordinates these processes. To determine how PelA modifies the polymer, we determined its structure to 2.1 Å and found a unique arrangement of four distinct domains. We have shown previously that the hydrolase domain exhibits endo-α-1,4-N-acetylgalactosaminidase activity. Characterization of the deacetylase domain revealed that PelA is the founding member of a new carbohydrate esterase family, CE21. Further, we found that the PelAB interaction enhances the deacetylation of N-acetylgalactosamine oligosaccharides. Using the PelA structure in conjunction with AlphaFold2 modeling of the PelAB complex, we propose a model wherein PelB guides Pel to the deacetylase domain of PelA and subsequently to the porin domain of PelB for export. Perturbation or loss of the PelAB interaction would result in less efficient deacetylation and potentially increased Pel hydrolysis. In PelA homologs across many phyla, the predicted structure and active sites are conserved, suggesting a common modification mechanism in Gram-negative bacterial species containing a functional pel operon.


  • Organizational Affiliation
    • Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PelA900Pseudomonas thermotolerans DSM 14292Mutation(s): 0 
UniProt
Find proteins for Q9HZE4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HZE4 
Go to UniProtKB:  Q9HZE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HZE4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.631α = 90
b = 93.582β = 90
c = 124.104γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata reduction
XDSdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP43998
Canadian Institutes of Health Research (CIHR)CanadaFDN154327

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release